FF-304 #comment Updates for the following 3 issues: FF-304 - accessio…

…ns generated for experiment sets (ES) FF-299 fixed type in enum of experiment_set.type for technical replicates FF-298 Added the sra database URL to namespaces.json

src/encoded/schema_formats.py

@@ -8,8 +8,8 @@
 )
 from uuid import UUID
 
-accession_re = re.compile(r'^4DN(EX|FI|FS|SR|BS|IN|WF)[1-9A-Z]{7}$')
-test_accession_re = re.compile(r'^TST(EX|FI|FS|SR|BS|IN|WF)[0-9]{4}([0-9][0-9][0-9]|[A-Z][A-Z][A-Z])$')
+accession_re = re.compile(r'^4DN(EX|ES|FI|FS|SR|BS|IN|WF)[1-9A-Z]{7}$')
+test_accession_re = re.compile(r'^TST(EX|ES|FI|FS|SR|BS|IN|WF)[0-9]{4}([0-9][0-9][0-9]|[A-Z][A-Z][A-Z])$')
 uuid_re = re.compile(r'(?i)\{?(?:[0-9a-f]{4}-?){8}\}?')
 
 @FormatChecker.cls_checks("uuid")

src/encoded/schemas/experiment_set.json

@@ -9,6 +9,7 @@
     "additionalProperties": false,
     "mixinProperties": [
         { "$ref": "mixins.json#/schema_version" },
+        { "$ref": "mixins.json#/accession" },
         { "$ref": "mixins.json#/uuid" },
         { "$ref": "mixins.json#/aliases" },
         { "$ref": "mixins.json#/status" },
@@ -21,6 +22,9 @@
         "schema_version": {
             "hidden comment": "Bump the default in the subclasses."
         },
+        "accession": {
+            "accessionType": "ES"
+        },
         "experiments_in_set": {
             "title": "Set of experiments",
             "description": "List of experiments to be associatedas a set.",
@@ -42,7 +46,7 @@
               "unspecified",
               "replicates",
               "biological replicates",
-              "technical repllicates",
+              "technical replicates",
               "analysis set",
               "publication"
             ]

src/encoded/schemas/namespaces.json

@@ -1,3 +1,4 @@
 {
-    "UniProtKB": "http://www.uniprot.org/uniprot/"
+    "UniProtKB": "http://www.uniprot.org/uniprot/",
+    "SRA": "https://www.ncbi.nlm.nih.gov/sra/?term="
 }